Mutations in the transcription factor SOX9 give rise to campomelic dysplasia, a syndrome characterized by skeletal abnormalities and XY sex reversal. Sox9 is expressed at sites of chondrogenesis and in the developing testis, and, thus, it plays a role in two overtly different pathways of differentiation. Previous studies have identified the gene for type II collagen, Col2a1, as a target of Sox9 in mouse chondrocytes and implicated Col9a3 as a Sox9 target in testis. Using differential expression analysis combined with reverse transcription-polymerase chain reaction and whole-mount in situ hybridization, we have identified nonchondrocytic collagen transcript isoforms that are expressed in the early male mouse gonad. Male-specific, gonadal expression of nonchondrocytic Col2a1 was first seen at 11.5 days postcoitum (dpc) and was undetectable by 13.5 dpc. This was accompanied by increasing expression of nonchondrocytic Col9a1, Col9a2, and Col9a3, first detected at 11.5 dpc. Expression was analyzed in testes that had been depleted of germ cells by the cytotoxic drug busulfan. These studies showed Col9a3 and Col2a1 to be expressed in Sertoli cells within the developing testis cords. Nonchondrocytic type II collagen contains a cysteine-rich domain that has been shown to bind members of the transforming growth factor β superfamily of signaling molecules. Thus, this interaction may play a role in the morphogenesis and differentiation of the testis.